The 1941 letter refers to testing and analysis of the product with the conclusion Jack Daniel's is not bourbon or rye whiskey. To me, this implies the agency found something in the product which disqualified it from being bourbon or rye. If the regulations defining the types of whiskey were the same in 1941 as now, and if something that is legally bourbon must be so styled on the label, this must mean there is something in Jack Daniels that does not conform to the definition of bourbon and rye. I theorise this could be extracts from the combusted maple wood the white dog spends some days (not just a few hours) leaching through. Perhaps residual maple sap enters the product. True, saps might come in to bourbon from charred oak containers but the regulations allow, indeed require, aging in new oak wood containers. I think a reasonable interpretation would encompass a subsequent filtration through oak-derived charcoal (for any bourbons which undergo that treatment). A neutral filter (the pad type decribed recently for filtering Four Roses Single Barrel, and possibly any deactivated charcoal) obviously adds nothing to the spirit and is neither here nor there in terms of flavor.
Now, if a whiskey to which maple wood derivatives are added must be redesignated, perhaps the very word, "Tennessee", supplies this need. Tennessee would mean, not (or not only) where the whiskey is made, but the style of whiskey it is (that which undergoes a preliminary maple wood charcoal leaching). On the other hand, perhaps Stewart Berkshire was saying in a polite governmental way that he tasted Jack (not chemically analysed it) and it doesn't taste like any bourbon he knows, hence it's distinctive. But if he was not referring to taste, or only to taste, but rather to what came out of the agency's physical analysis, what was it that made him think it wasn't bourbon or rye? I cannot think of anything other than maple wood derivatives. I note George Dickel's whiskey also states, "Tennessee" on the label; it too undergoes the maple charcoal leaching, so a similar logic might apply here too..
In sum, it seems to me either something must be "added" to these whiskeys (I surmise, maple wood extracts) to take them out of the definition of bourbon and rye or they ARE legally bourbon yet are not required so to state on the label. The latter possibility seems ruled out however by the regulation referred to earlier in the thread requiring that a defined whiskey type must be declared (on the bottle) by the maker. Unless, possibly, the rules mean it is sufficient to use the name of a set (whiskey) and not the subset (bourbon) to style the product.
I have not reviewed the regs in full but offer these thoughts after reading the last few posts.